Lack of trust
by johnliz4ever
Summary: When a off world mission goes wrong and Dr Weir is attacked all evidence points at Bates'.
1. Chapter 1

Disclaimer: I don't own the boys and girls at Stargate Atlantis

Note: I swear my brain doesn't know when to shut off. I started writing this at about midnight  
Warning: Implied attempted rape

**Karan **

Elizabeth, Bates, Ford, Rodney and Teyla sat at the banquet table of their new trading partners the Karans.

Elizabeth, who was sat between Bates and Commander Phylis, started feeling dizzy.

Bates turned to Elizabeth and saw her holding her head.

"Dr Weir, are you alright?"

Elizabeth nodded weakly.

"Why is the room spinning?"

Bates become worried and placed his hand on her shoulder

"Dr Weir, are you okay?"

Elizabeth shook her head this time.

"I don't feel very well. I think I'm going to get some sleep."

Elizabeth started to stand up, instantly going dizzy again. Bates quickly stood up and held her lightly to support her.

"I'll take you, make sure you get there"

Elizabeth smiled in thanks before the two of them turned to face Commander Phylis.

"Will you be rejoining us St Bates?"

Bates shook his head, still supporting Elizabeth.

"No, I think I'm going to turn in too."

Commander Phylis nodded and smiled politely.

"Well goodnight"

Bates nodded and slowly helped Elizabeth to the room the Karans had set aside for her. Despite the fact that Elizabeth got confused about where her room was they eventually found it.

Bates was actually quite amused that Elizabeth couldn't hold her drink and that she would be paying for it in the morning, however he hadn't really seen her drink much and he'd been keeping an eye on her all night.

Bates snapped out of his musing and opened the door to Elizabeth's room, helping her inside and over to the bed in the middle.

He laid her down gently, his hand brushing across her rips as he pulled away from her. He placed the covers over her and brushed away a piece of her hair before stepping away from the bed.

"Will you be okay Dr Weir?"

Elizabeth nodded.

"I will. Thank you St Bates"

Bates nodded and headed for the door.

"Goodnight Dr Weir"

Elizabeth snuggled down into the bed. She was still for a few moments until she felt a hand brush through her hair.

"You're so beautiful"

Elizabeth opened her eyes in a panic but the room was too dark to make out anything but shadows and shapes.

"St Bates"

Elizabeth was shocked and sickened when a mouth invaded hers, slipping a tongue passed her lips and into her mouth. She quickly turned her head away from the mouth.

"No, stop it"

She tried to move but felt increasingly weak, even more so when someone sat on her lower stomach, effectively pinning her to the bed.

Elizabeth couldn't see anything but darkness and shapes but she could feel everything.

She could feel his rough hands over her body, on her stomach, moving upwards underneath her shirt to her breasts.

Elizabeth gathered all the strength she could and tried to push off her assailant, this resulted in her being hit and nearly strangled until she stopped moving and struggling.

Elizabeth frantically thought of a way she could end this. She knew what would happen if she didn't.

In a quick and unexpected move, Elizabeth rose her hands and scratched her assailants' left cheek with her nails, while he was distracted and temporarily stunned she forcibly pushed him off and sprung off the bed, running from the room as quickly as she could. She ran down the corridor until she bumped into someone. Elizabeth looked up, relieved at who she saw.

"Teyla"

Teyla was shocked by Elizabeth's appearance. Her neck was red with a hand impression settling in; she was bleeding from her head and had a black eye appearing as well as over small cuts and bruises.

"Dr Weir, what happened?"

Elizabeth replied with only one word.

"Bates"

* * *

Bates whistled to himself quietly as he got ready to turn in for the night. 

As he was about to shut off the light, the door to his room burst open and a very angry Lt Aiden Ford stepped in.

"Sir, what can I do for you?"

He barely finished his sentence when Ford's fist connected with Bates' jaw.

"You son-of-a-bitch"

Ford shouted at him, he was about to go for another swing when Rodney rushed into the room and grabbed his arm. Bates had never been so happy to see the scientist.

"He's not worth it. He's not worth it"

Ford swallowed hard and nodded, lowering his fist. Bates stumbled to his feet after being knocked down by the force of Ford's punch.

Markham and Stackhouse entered the room; Ford spoke to them, not taking his eyes off Bates.

"Arrest him, take him into custody"

Bates tried to fight against Markham and Stackhouse but they overpowered him.

"What the hell for?"

Ford walked right up to him, staring at him like a hungry Wraith stares at their next meal.

"You know damn well. For attacking Dr Weir you bastard"

Bates stared at Ford in shock as he was taken from the room.

* * *

**Atlantis **

"I miss one mission and she gets attacked."

John shouted at his team, not angry with them but angry at the whole situation.

John looked over at Ford who had a bandage on his left hand.

"I'm going to have to discipline you for hitting him"

Ford shrugged

"I did what I thought you would do"

John shook his head in disbelief and sighed.

"Ford, you gave the guy a concussion"

Ford smiled slightly.

"Exactly, I did what I thought you would do"

John nodded slightly realising that the kid was right. If John was there he'd have done the same thing.

"I lost it, I saw her all bruised and fragile and I just lost it. I'm sorry sir"

John sighed, shifted in his seat and looked over at Teyla who was staring at the table in front of her, not acting her like her usual self.

"Teyla"

Teyla didn't respond, she continued to stare down at the table. John called her name again, this time a little louder.

"Teyla"

Teyla looked up at him suddenly, confusion on her face.

"Yes Major?"

John shook of her confusion; there were more pressing matters at hand.

"How is Eliz…Dr Weir doing?"

Everyone in the room noticed the slip up but nobody questioned it.

Teyla sighed gently.

"Physically it is no more than cuts and bruises which should heal in time, mentally and emotionally, I can not be sure. Her spirit and trust seem damaged and Dr Heightmeyer as already requested to see her."

John nodded sadly

"Teyla, you were the one who found her, right?"

Teyla nodded

"Tell us what happened"

Flashback (**Karan)**

"Bates"

Teyla held Elizabeth lightly,

"What did he do?"

Elizabeth didn't answer, she just got increasingly fussy and Teyla decided to take her somewhere safe and contact Ford and Rodney.

Teyla helped Elizabeth to her room and sat her down on a chair near the door; she bent down in front of her and noticed that Elizabeth's breathing seemed to be returning to normal. She picked up her radio and contacted Ford.

"Lt Ford this is Teyla, can you and Dr McKay come to my room, there is a situation"

"_We'll be right there Teyla"_

Sure enough within about five minutes, Ford and McKay were at Teyla's room. Teyla had called them both because she knew it was a situation Ford would have to deal with but she also knew Elizabeth might be more receptive to McKay.

When Ford and McKay entered, the room entered the room Elizabeth didn't even seem to notice.

McKay bent down in front of her placing his hand on her knee. Very quickly Elizabeth shifted her legs away from him and McKay stood up and looked at Ford.

Ford nodded and walked over to Elizabeth.

"Dr Weir, what happened?"

Elizabeth looked over at him, he could tell she was trying hard to be strong and for the first time he could see the marks on her face and neck.

"I thought…I thought he'd gone, I…I heard someone walk over to me."

Ford bent down in front of her.

"Teyla said that you mentioned Bates. What about Bates?"

Elizabeth tried to turn away from him but he grabbed her chin lightly and made her face him.

"Elizabeth…"

Elizabeth began to shake.

"It was him, it was Bates"

Ford stood up quickly; he ran a hand across his face. McKay looked at him, slightly worried

"Ford?"

Before anyone could do anything Ford bolted out of the room and McKay was on his radio to Markham and Stackhouse, following him. Teyla watched as they left the room, before she allowed her eyes to fall back onto Elizabeth.

End of Flashback 

"I don't believe I have ever seen Dr Weir look so afraid."

John nodded and looked down,

"In his statement Bates said that Weir was pretty out of it. Do any of you think that she may have made a mistake?"

Ford shook his head immediately

"I don't think so, she's pretty observant and she seemed so damn sure"

John turned to Rodney and he shrugged

"I don't know."

John turned to Teyla who lowered her head

"Dr Weir was most upset. It is possible she made a mistake."

All the men in the briefing room turned to her

"I am not saying that she made it up, but what would St Bates have to gain by attacking her?"

The three men knew she had a point but were stunned that Teyla was the one standing up for Bates, the two of the hated each other.

John stood up.

"Well DNA will confirm if it was Bates. Beckett is running that now. Until than get some rest and Ford, I'm taking you off active duty till I see fit"

Ford nodded knowing that he had to have some sort of punishment for his outburst

"Yes Sir"

John then walked out of the room leaving his team alone.

* * *

John walked into the infirmary and saw Beckett over at his desk looking at a piece of paper. 

He walked over to him and sat down opposite.

"Do I want to know?"

Beckett handed the paper over to John and sighed

"His DNA was all over her, over her clothing and her body"

John threw the paper onto the table.

"That son-of-a-bitch"

Beckett picked up the paper, which John had just threw and placed it neatly on a pile.

"Have you spoken to Dr Weir?"

John looked up at him and sighed

"No, I thought it best to give her some time."

Beckett nodded and looked at him

"She needs you Major."

John looked back down at the table

"What am I suppose to say? Sorry I assigned the guy that tried to rape you, it won't happen again"

Beckett sighed.

"You didn't know what would happen. You assigned Bates to your team for that mission because he is a good officer."

John nodded but still looked down

"I should go talk to him"

John stood up and left the infirmary leaving Beckett to contemplate what would happen next.

TBC…


	2. Chapter 2

Disclaimer: I don't own the boys and girls at Stargate Atlantis 

Bates sat in the small cell which John had ordered him to, continuing to feel extremely pissed. None of the guards assigned to watch over him were saying anything. He didn't really know what had happened. He knew Elizabeth had been attacked, and he overheard something about her nearly being raped, but why the hell would they think it was him.

Bates continued to run though the thoughts in his mind when he saw John walk into the room. He stopped and looked at him for a few moments before stepping over to the bars.

Bates stood up and walked over to him.

"Sir, this as been a big mistake I never..."

John cut him off, obviously pissed

"Shut the hell up Bates. You better start telling the truth, why did you attack Dr Weir?"

Bates sighed and looked John straight in the eye.

"I never attacked Dr Weir"

John shook his head

"Bates, don't lie to me, we have your DNA all over her clothing and body, she told us it was you"

Bates shook his head

"I didn't touch her. I could never do that to her or any other woman for that matter."

John sighed

"Okay, if you didn't do it would you like to explain how your DNA got on her."

Bates sighed and began.

"Dr Weir wasn't feeling well, she said she wanted to go back to her quarters. I didn't think she would get there without collapsing, she was deathly pale and the Stargate was too far away so sending her back to Atlantis was out of the question, so I offered to take her back to her room..."

**Flashback**

Bates quickly stood up and held Elizabeth lightly to support her.

"I'll take you, make sure you get there"

Elizabeth smiled in thanks before the two of them turned to face Commander Phylis.

"Will you be rejoining us St Bates?"

Bates shook his head, still supporting Elizabeth.

"No, I think I'm going to turn in too."

Commander Phylis nodded and smiled politely.

"Well goodnight"

Bates nodded and started to walk with Elizabeth.

The room said aside for her was quite out of the way, and Elizabeth was very tipsy. Bates, fearing she would fall slipped a hand around her waist and held her closely. Elizabeth dropped her head onto his chest and yawned. Bates was stunned by the action and nearly dropped her.

"Dr Weir"

Elizabeth looked at him and was suddenly aware of her proximity to him, she blushed and pulled away slightly.

"Yes, of course, sorry"

Bates chuckled slightly and tightened his grip, barely noticing when his hand slipped underneath her shirt.

**End of flashback**

John looked at Bates not entirely convinced of his story.

"So you're saying that your hand, slipped under her shirt"

Bates nodded,

"That's what I'm saying"

John shook his head

"Cut the crap Bates, your DNA was everywhere, not just on a small section of her skin. Tell me the truth Bates, what are you hiding?"

Bates sighed and looked away

"Do you really want to know? I can assure that you will be pissed."

John nodded

"Try me"

Bates sighed and looked back up at him

"Dr Weir...she came on to me. Sir she was wasted, she didn't know what the hell she was doing. I said no. I pushed her away and said no, but she was pretty insistent. I had to push her away, that's how my DNA got onto her. By the time I got her back to her room, she didn't even remember it had happened but I didn't touch her"

John nodded and looked at Bates

"I'll check that out. But if I find out that you're lying, I'll be back"

Bates shook his head

"I'm not."

* * *

John stood outside of Elizabeth quarters and nervously knocked on the door. There was silence for a moment before he heard a hesitate 'Come In'. 

John opened the door and saw Elizabeth stood at the window in her quarters.

He walked to where she was stood but stayed a good distance away, so not to spook her.

"Dr Weir"

Elizabeth turned to face him

"Major"

Her face was still covered in busies and the black eye was still forming but it was already a dark blue colour.

"Dr Weir, I have to ask you about what happened?"

Elizabeth turned back to the window.

"I have told you everything."

John nodded and was about to walk closer to her before thinking better of it.

"Elizabeth I've talked to Bates…"

John saw Elizabeth shiver as he said that name, but only ever so slightly and only for a moment.

"…He said some stuff that I need you to confirm or deny."

Elizabeth stayed looking out of the window

"What do you need to know?"

John cleared his throat.

"Elizabeth, I…I need to know what you remember from last night."

Elizabeth ran a hand through her hair and sighed.

"We had dinner Karans. Near the end of dinner, I started to feel dizzy. Bates' took me to my room. It was dark, I couldn't see very well. I heard…I felt someone come back into the room. I called out, nobody answered. He told me I was beautiful. It was Bates' voice."

Elizabeth stopped for a moment and John looked over to her, she was staring blankly out of the window.

"Then he kissed me. I tried to push him away but he was too strong."

Elizabeth stopped sharply and turned to John.

"Why do you need to know all this? I've already told you what happened. All I want to do is get back to work and forget this happen."

John was about to take a step forward but thought better of it.

"Elizabeth, please don't hate me for what I'm about to ask." John paused for a moment. "Elizabeth, is there any chance that you…that Bates' could have thought that was what you wanted"

Elizabeth looked at him disgusted.

"Absolutely not. No. How could you even say that?"

John sighed in frustration

"Look, I don't believe that, but Bates' said that you came on to him, he said you were drunk. He said you were all over him but he denies trying to…hurt…you"

John couldn't bring himself to say the word 'rape'. He couldn't bare to see her hurting anymore.

Elizabeth looked up at the ceiling before realising something about what John had said.

"I wasn't drunk. I…I had about half a glass of particularly weak wine, but I wasn't drunk. I was ill."

**Infirmary **

Carson handed John the toxicology report he had ordered on Elizabeth.

"Positive for a date-rape drug."

John shook his head.

"Bates, you bastard"

Carson cut in.

"Aye, that might be a problem. The drug…while yes it is still date rape…it is different to what would might find on Earth. This is Alien, relatively same effects thought this is faster and easier to use."

John was about to respond when he received a frantic call on his radio from Rodney.

"Major, I've just found unconscious in her quarters."

Carson hit the button on his radio.

"I'll be right there"

Carson grabbed some supplies and ran out of the infirmary followed by John.

**Elizabeth Quarters **

Carson brought a glass of water to Elizabeth's lips and she gently sipped the water.

By the time, Carson and John had made it to Elizabeth's quarters after Rodney had contacted them she was already coming round and slightly confused by what had happened.

Carson put the glass on the bedside table.

"You sure you don't want a wee more to drink?"

Elizabeth shook her head.

"I'm okay"

Carson nodded and proceeded to check her temperature again which was slowly going back down to normal.

"Well you seem as right as rain now. If you start feeling dizzy or you get a headache I want you to come and see me"

Elizabeth nodded and Carson walked away from her and over to John, grabbing his arm and dragging him to the back of her room while Rodney tried to make polite conversation with Elizabeth without freaking her out.

"I have a feeling her body is beginning to expel the drug, that's why she collapsed."

John nodded

"We don't tell her. At least not yet…she already feels weak, we don't need to make that worse."

"If you two are talking about me I would appreciate it if you didn't whisper, I have a right to know."

Elizabeth's voice was strong and commanding, causing both men to look at her. Carson sighed and walked back over to her.

"Elizabeth. I did a toxicology test; there are traces of compounds that make up a date-rape drug, in your system. Your recent collapse and the high temperature and sweating are your body's way of trying to expel the drug from your system,"

Elizabeth nodded calmly.

"If you don't mind I think I want to get some sleep."

Carson and John nodded and proceeded to leave the room; Rodney hung back for a bit and turned to Elizabeth.

"If there's anything you need or want from anywhere, just let me know. Even if you just want someone to talk to, I'll be on radio."

Elizabeth smiled in gratitude.

"Thank you Rodney"

Rodney offered her a smile and started to leave her quarters, he was about to turn off the light until her voice stopped him

"Rodney, leave the light on please"

Rodney turned round and nodded before leaving her quarters.

**Gym**

John walked into the gym to see Teyla already there training. He walked over to the side and set his bag down as Teyla looked over at him.

"Major, I did not expect you to be training today"

John sighed and sat down.

"I need to do something to get my mind off what's happening."

Teyla nodded

"I know. Dr Weir is such a strong woman, but this…this as left her feeling weak. Weaker then I thought she could ever be"

John nodded and stood up just in time to see Teyla go dizzy. Quickly he grabbed her arm and held her upright.

"Teyla, are you okay?"

A layer of sweat started to form across Teyla's forehead and her words slurred out before she started to fall sideways.

John grabbed her and set her gently to the floor. Grabbing his radio, he contacted Carson.

"Carson, Teyla's just collapsed"

TBC…


	3. Chapter 3

Disclaimer: I don't own the boys and girls at Stargate Atlantis

* * *

Ford and John sat in the infirmary waiting for news on Teyla. Carson found her symptoms eerily similar to Elizabeth's when she collapsed so he was running some tests, hopefully to rule out that someone had drugged her as well. 

Carson finally emerged causing Ford and John to stand up and look at him.

"I found the same drug in Teyla's system. Smaller quantities though. That's why it took longer for her symptoms to show"

John stood confused for a moment

"Why would Bates' drug Teyla as well? It doesn't make any sense"

At that moment, Rodney walked into the infirmary with Elizabeth. Elizabeth had heard over her radio what had happened to Teyla and contacted Rodney to see if she was okay. When he said that he wasn't sure she had straightened herself out and made her way down to the infirmary. She was no longer the only victim.

"We shared some wine. I had too much in my glass so I offered Teyla some. She only drank a small amount."

John stepped forward to Elizabeth.

"Elizabeth you should be…"

Elizabeth cut him off

"I should be what John? Resting, hiding, snivelling. No, I won't do that, not anymore. I will not let it beat me"

Behind Elizabeth, Rodney was smiling at her strength and courage to carry on, to not be a victim but to stand strong.

John sighed and nodded

"Okay."

Elizabeth nodded and turned to Carson.

"How's Teyla feeling?"

"Her temperature's down and she's not as pale as she was"

Elizabeth nodded

"Can I see her?"

Carson nodded

"Aye"

Elizabeth smiled and walked past him towards Teyla. John looked over at the rest of the group and sighed.

"Well, I guess that rules Bates out."

Ford shrugged

"Not necessarily. We only know the drug is not from Earth. It's possible that he found it on Karan"

John sighed and rolled his neck to the size working a kink out of it.

"Carson, can you get me a sample of the drug that you found in Elizabeth's blood. I want to go to Karan, see if they can identify who bought the drug."

Carson nodded and went into his office leaving John, Rodney and Ford looking over to where Elizabeth had just disappeared to see Teyla.

Ford cleared his throat.

"You don't think...that Dr Weir...well you don't think she's trying to do too soon, do you?"

John sighed

"Elizabeth will try not let it affect her, she won't let it show. At least not to any of us"

Rodney nodded

"But maybe to Teyla"

John shrugged

"Maybe"

* * *

Only a few feet away Elizabeth sat down on the chair which was next to Teyla's bed. Teyla opened her eyes and smiled at Elizabeth. 

"Dr Weir"

Elizabeth smiled weakly

"I'm so sorry Teyla"

Teyla shook her head.

"You have nothing to be sorry about. Nothing happened to me"

Elizabeth shrugged

"But something could have."

Teyla placed her hand on Elizabeth's

"Elizabeth, listen to me. You may think that you should feel guilty, but you did nothing wrong and there was nothing you could have done to prevent your attack. Do not feel guilty for something that was out of your control"

Elizabeth slowly nodded as she listened to Teyla's words. As she listened to the faith she had in her.

"Thank you Teyla"

**Karan**

When John, Rodney, Stackhouse and Markahm arrived on Karan they was met by Commander Phylis, who smiled at them.

"Major Sheppard. It is an honour to see you again. Please tell me how is your Dr Weir?"

His voice was full of concern for the Atlantis leader and John felt touched by it.

"She's doing better."

Commander Phylis nodded.

"Please send her my best wishes"

John nodded and smiled at him.

"I will"

Commander Phylis nodded.

"I believe you wish to speak to our medicine man, he is in the village at the moment but he is undergoing a spiritual cleansing and must not be disturbed, but I would be grateful to help you with anything you need to know."

John nodded

"Okay, we need to know what you saw that day."

Commander Phylis nodded.

"Of course. Please follow me to my home. We will be more comfortable there."

John nodded and the team followed Phylis to a lavish house on the outskirts of the small village.

They all sat in the kitchen of the great house before Phylis began.

"I did see Dr Weir with St Bates quite a lot over the course of the day. During a brief amount of time, perhaps an hour he disappeared leaving Elizabeth with your Lt Ford. I did not suspect anything at the time. During the evening, well he spent the most time with her. He brought her a glass of wine and sat with her a dinner…"

John cut him off

"Hold up, he brought her the wine"

Commander Phylis nodded

"Yes."

John sighed

"Did she drink anything else other than that wine?"

Commander Phylis shook his head.

"No, she seemed to sip that one drink all night."

John could practically hear Rodney behind him ready to snap Bates' neck

"Tell me about when Dr Weir became ill"

She was sat between myself and St Bates. She started to go dizzy and St Bates said that he would escort her back to her room. I asked if he would be rejoining us and he said no, he had a look in his eyes, I didn't think anything of it. The way he talked to me about Dr Weir at one point…well I thought they were pending joining"

Rodney looked in confusing and Stackhouse whispered to him

"He thought they were to be married"

Rodney nodded but then stopped at the thought and shuddered before speaking up.

"Did he say that?"

Phylis shook his head

"No, but he did not deny it either, he just smiled when I asked him"

John buried his head in his hands.

"When can we talk to the medicine man?"

Phylis sighed

"I do not know. Spiritual cleansing can last for days at a time. I will inform you when he is back with us"

John nodded

"Thank you"

**Atlantis**

The team arrived back on Atlantis none the wiser about what really happened. All they could ascertain was that Bates' spent a lot of time around Elizabeth and that Phylis thought they were engaged. Sighing John entered the cell area and set out all the guards watching Bates'. He then pulled over a chair and sat down, staring at Bates.

"Bates, this thing is really started to annoy the hell out of me. I've got one half of the Atlantis population wanting to snap your neck and the other half wanting to chop off your manhood. Then there's Kavanagh, the sick bastard, who wants to shake your hand for making Elizabeth weak.

I want this over Bates. Tell me, did you give Dr Weir the only glass of wine she drank"

Bates sighed

"It was the first glass of wine she had, but how drunk she was says to me that it wasn't her only glass"

John nodded

"Dr Weir said she was ill, not drunk"

Bates shrugged

"Maybe she was ill, I don't know."

John sighed

"Where did you get the glass of wine that Dr Weir drunk?"

"A table, the medicine man was stood there, we talk for a while and he poured me the drinks"

John did a double take

"The medicine man, are you sure?"

Bates nodded

"Yes"

John quickly stood up and left the cells contacting Rodney on his radio.

"Rodney, suit up, we've got ourselves a medicine man to find"

**Karan**

Phylis was shocked when John and the team arrived back on the planet.

John walked right over to him and felt like punching the Commander.

"You lied to me; you are protecting the medicine man"

Phylis lowered his head.

"I am sorry. He came to me, he confessed to attacking Dr Weir. I was so disgusted with him, I did not know what to do, he showed remorse and said he would undergo the spiritual cleansing if I would keep him safe from your people. He is scared."

John sighed

"Why did he attack her?"

Phylis sighed.

"He said that he as never seen a beauty such as Dr Weir, he said demons invaded his mind, told him to make that beauty his. He is very sorry for the pain he as caused both Dr Weir and St Bates. Please, do not let this come between the alliance of our two peoples."

John sighed

"I will have to talk to Dr Weir about that"

Commander Phylis nodded

"Of course and please, send her my deepest apologises. I did not mean this to go as far as it did"

John nodded and dialled the Stargate back up to Atlantis before stepping through.

When he was alone Commander Phylis headed back down to the village but instead of going to his home he carried on. He walked into the woods to a small hut. He walked in to see the medicine man tied and gagged.

Phylis smirked

"They believe it was you, and you shall not tell them any different"

Phylis took the gag off the medicine man.

"They will discover the truth Phylis. You have set me up"

Phylis smirked

"They will discover the truth, but by then it will be too late."

TBC…

I think that the next chapter will be the last.


	4. Chapter 4

Disclaimer: I don't own the boys and girls at Stargate Atlantis 

Elizabeth sat in her quarters listening to John as he told her what he had found out on the planet about the medicine man, Phlieep.

Elizabeth, though was not entirely convinced. Doubt still riddled in her mind.

"John, I met Phlieep. He was just like Carson. He's not...he's not a rapist John"

John sighed

"Elizabeth he confessed to Phylis."

Elizabeth sighed

"Did you hear him confess, did you see a sighed confession?"

John shook his head

"Why would Phylis lie? What would he have to achieve?"

Elizabeth sighed and sat down. John watched her for a moment before continuing.

"I have ordered Bates' release. We can't keep him locked up"

Elizabeth nodded.

"Send him to my office, I need to speak with him"

John nodded and left her quarters."

* * *

John walked into the holding room and ordered the door to Bates' cell to be opened. 

Bates curiously left the cell and stood in front of John.

"What's happening?"

John sighed and took a step back.

"The medicine man on Karan confessed to attacking Dr Weir. They are punishing him though their court of law."

Bates nodded.

"Told you I didn't do it"

John nodded.

"Go to Weir's office. She wants to see you"

Bates sighed and nodded before leaving the cell room.

**Elizabeth's office**

Bates hesitantly knocked on the door to Elizabeth's office. She looked up and gestured him in.

As Bates walked in he saw for the first time the extent of Elizabeth's injuries, her bruised cheek and her black eye.

He was still angry and annoyed with her, but seeing her like this softened him.

As he entered her office Elizabeth stood up.

"St Bates"

Bates nodded

"Ma'am"

Elizabeth gestured for him to sit down and Bates did so. Elizabeth sat opposite him and sighed.

"Bates, I am so sorry for assuming it was you but...I thought I saw you"

Bates nodded

"It hurt,"

Elizabeth nodded

"I am sorry"

Bates sighed

"I know"

Elizabeth was about to respond when the alarms went off. Elizabeth ran out to the control room and stood beside Peter.

"Peter who is it?"

Peter looked over at the IDC computer.

"It's the Karan's Ma'am. It's a radio message."

Elizabeth nodded

"Patch it thought"

Peter nodded and hit a button to allow the radio transmission to come though.

"Major Sheppard this is Commander Phylis of the Karan's. I have news for you."

Elizabeth cleared her throat.

"What's the problem Commander?"

"Dr Weir. It is good to hear your voice. I have news for you. May I please come though the Stargate?"

Elizabeth turned to Peter and nodded. Peter turned the shield off and Elizabeth turned back to her conversation with Phylis.

"The shield is lowered. You may step though"

A few seconds later Commander Phylis stepped through the 'Gate.

Elizabeth walked down the stairs to him.

"Commander, What's the problem?"

The Commander looked at Elizabeth sympathetically

"I know what you have been through and I apologise about keeping what I knew from Major Sheppard, but the medicine man, the one who attacked you has taken his own life."

* * *

John, Elizabeth and Commander Phylis sat in the briefing room. 

Commander Phylis was talking of how they found Phlieep, the medicine man.

"He regretted what he did to you. He was sorry for getting St Bates in trouble"

Elizabeth sighed

"What happened to him?"

Phylis looked at her for a while before responding.

"After the spiritual cleansing he returned to a holding house where he would stay to pay for his crime. When we arrived back in the morning, he had hung himself"

Elizabeth looked down in guilt before standing up and excusing herself and leaving the room.

Commander Phyis' eyes watched Elizabeth as she left the room before he looked back at John.

"I am sorry if I have upset Dr Weir"

John shook his head.

"It's not your fault. She's still trying to work though it."

Commander Phylis nodded

* * *

Elizabeth sat down on the bed in her quarters. She had been so sure it was Bates'. How could she have been so wrong. 

She sat in silence for a few moments until she heard a knock on the door.

Slowly she walked over to the door and opened it, shocked to see Commander Phylis standing there.

"Commander, what are you doing here?"

Phylis smiled at her.

"I hope I have not caused you upset."

Elizabeth shook her head.

"No, no I'm fine"

Something suddenly struck Elizabeth.

"Why do you not have an escort?"

Phylis' smile turned into a smirk as he quickly pushed Elizabeth into her room, hitting the door closing switch.

He pushed her to the floor and sat on her, pinning her to the floor where he trapped her arms underneath her body.

As Elizabeth struggled to get free she saw something on his neck. A scratch. A scratch she caused.

* * *

John bumped into Bates' in a corridor as he jogged round. 

"Bates' have you seen Commander Phylis. I turned round for a second and now he's missing."

Bates' thought for a second, before something hit him.

"Dr Weir, he was the one who attacked her"

John shook his head.

"What?"

"You never spoke with the medicine man and now he's dead. Who told you about his confession? Who said I was the one who was giving Dr Weir drinks and paying attention to her."

The colour drained from John's faces as he realised Bates' was right.

In a flash the two men bolted from their position in the corridor and down to Elizabeth's quarters, calling for Rodney, Ford and Carson on the way.

* * *

Elizabeth struggled under the weight of Phylis. 

"I will not let you escape me again. The drug I gave you was suppose to make you more relaxed. I didn't anticipate that you would fight it. I will not make that mistake again"

Phylis took a needle out of his pocket and placed it near to her neck. As he was about to inject her the door opened. Bates' and John rushed into the room knocking the needle from his hand and pulling him off Elizabeth.

As John checked Elizabeth over Bates' threw Phylis against the wall and punched him as hard as he could. When John saw what Bates' was doing he stood up and grabbed his arm.

"No, Bates. He's not worth it"

Bates' pushed him against the wall one last time before withdrawing back.

He turned round and saw Elizabeth still sat on the floor. Huddled next to the bed. Slowly he walked over to the bed and sat down next to her. Carefully he placed his arm around her. She tensed for a moment before relaxing into him. She didn't cry, he didn't expect her to, but he could tell she wanted to.

Within a few minutes Carson walked into the room. He totally ignored the man with broken jaw and black eye and went straight over to Elizabeth. Bates' moved away from her and went over to where John was standing.

"Thank you Bates', for figuring it out. If you hadn't..."

Bates' nodded

"Not a problem."

**A few weeks later**

Although they were shocked the other leaders of Karan had decided on a punishment for Phylis and they were currently executing it.

Elizabeth, she was still having the nightmares, nightmares in which John and Bates didn't arrive in time and that Phylis raped her. She was having a difficult time but she was talking with Kate on a regular basic and Kate was confident that Elizabeth was making some progress.

Bates had forgiven Elizabeth for accusing him, after seeing how scared she was after Phylis' second attack it was obvious she hadn't been thinking straight and that's how she came up with the conclusion it was him.

Bates was sat in the mess hall drinking a coffee like drink which was much more heavily caffeinated.

He sat there alone until someone walked up and sat down opposite. Bates looked up to see John.

"Major Sheppard"

John nodded

"Bates. I just wanted to say, sorry. I know it's a little late but I mean it. Sorry I treated you the way I did."

Bates' nodded

"You thought I was guilty of attacking Dr Weir. I would have done the same to you"

John smiled

"Don't doubt that for a second."

John stood back up and left Bates with his thoughts.

Fin...


End file.
